Doctor of Philosophy
The Polycomb group (PcG) proteins form two protein complexes, Polycomb repressive complex 1 (PRC1) and PRC2, which are key epigenetic regulators in eukaryotes. PRC2 represses gene expression by catalyzing trimethylation of histone H3 lysine 27 (H3K27me3). In Arabidopsis thaliana, CURLY LEAF (CLF) and SWINGER (SWN) are two major H3K27 methyltransferases, playing essential roles in plant growth and development. Despite their importance, genome-wide occupancy profiles of CLF and SWN have not yet been determined and compared. In this thesis, I generated transgenic lines expressing GFP-tagged CLF/SWN and determined the genome-wide distributions of CLF and SWN in Arabidopsis seedlings. I also compared the global H3K27me3 levels in wild-type (WT) and PcG mutants (clf, swn, and clf swn). The data show that CLF and SWN co-targeted a large number of genes, except that SWN had a few hundred more targets. The GAGA-like and Telo-box-like motifs were found enriched in CLF- and SWN-occupied regions. The global H3K27me3 levels in clf, but not in swn, were markedly reduced compared to WT, and H3K27me3 was undetectable in clf swn. Thus, this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC2 in plant growth and development.
SPLAYED (SYD) is an SWI/SNF-type chromatin remodeler that plays critical roles in the regulation of gene expression. SYD is the closest homolog of BRAHMA (BRM), functioning redundantly and/or differentially with BRM in Arabidopsis. Recently, the genome-wide occupancy of BRM has been profiled. However, the occupancy of SYD was still missing. Therefore, I generated a transgenic line expressing GFP-tagged SYD which was used for profiling the genome-wide occupancy of SYD at the seedling and reproductive stages. SYD and BRM co-localized at over three thousand genes, suggesting that SYD and BRM function redundantly at these genes. When analyzing the global distribution of H3K27me3 in syd, it was discovered that the loss of SYD activity resulted in changes in H3K27me3 levels at over several hundred genes compared to WT. To summarize, this work demonstrates the genome-wide occupancy of SYD and emphasizes a global functional interplay between SYD and PcG repression.
Summary for Lay Audience
A seed can develop into a whole plant that has many different tissues. However, every cell has the same genome containing the same genes. In general, it is the expression levels of genes that contribute to the production of different cell types, thereby different tissue types. There are many proteins playing important roles by changing the expression levels of different genes. In this thesis, I focus on examining two types of proteins by using a model plant organism Arabidopsis thaliana. These two types of proteins play very important roles in plants, as plants cannot grow normally when the functions of genes (encoding these two types of proteins) are disrupted.
The first type is the Polycomb group (PcG) proteins. They usually form two complexes: Polycomb repressive complex 1 (PRC1) and PRC2. PRC2 lowers gene expression levels by adding three methyl groups to histone H3 at lysine 27 residue (referred to H3K27me3). PRC2 complex has two key subunits called CURLY LEAF (CLF) and SWINGER (SWN), which can change expression levels of different genes by producing H3K27me3 in plant cells. Therefore, it is important to find genes whose expression levels are controlled by CLF and SWN. Thus, in this thesis, I conducted experiments to find CLF- and SWN-controlled genes. Further, I also found that CLF and SWN function similarly in controlling expression levels of genes in plants. The second type is SPLAYED (SYD) which can change chromatin structures. SYD plays important roles in plant growth and development, as plants grow abnormally when SYD function is removed. Finally, I found many genes that are controlled by SYD. Previous literature proposed that there is interplay between SYD and PRC2. Therefore, I also examined the interplay between SYD and PRC2. My data suggest that SYD and PRC2 play opposite and/or cooperative roles in controlling gene expression levels in plants.
Shu, Jie, "Genome-wide occupancy of Polycomb group proteins and chromatin remodeler SPLAYED and their interplay in Arabidopsis" (2019). Electronic Thesis and Dissertation Repository. 6564.
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